Citing the TPP

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Revision as of 04:31, 9 August 2018

If you use the TPP or any of its components in your research, please cite us in your publications. Below is a list of citations categorized by topic.

TPP Overall Latest Paper

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics.

Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL.

Proteomics Clin Appl. 2015 Aug;9(7-8):745-54. doi: 10.1002/prca.201400164. Epub 2015 Apr 2. Review.

PMID: 25631240

TPP Overall First Paper

A uniform proteomics MS/MS analysis platform utilizing open XML file formats.

Keller A, Eng J, Zhang N, Li XJ, Aebersold R.

Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2.

PMID: 16729052

iProphet and Combining Search Results Review

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.

PMID: 21876204

Combining results of multiple search engines in proteomics.

Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.

Mol Cell Proteomics. 2013 Sep;12(9):2383-93. doi: 10.1074/mcp.R113.027797. Epub 2013 May 29. Review.

PMID: 23720762

PeptideProphet

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Keller A, Nesvizhskii AI, Kolker E, Aebersold R.

Anal Chem. 2002 Oct 15;74(20):5383-92.

PMID: 12403597

ProteinProphet

A statistical model for identifying proteins by tandem mass spectrometry.

Nesvizhskii AI, Keller A, Kolker E, Aebersold R.

Anal Chem. 2003 Sep 1;75(17):4646-58.

PMID: 14632076

Kojak for Cross-linking analysis

Kojak: efficient analysis of chemically cross-linked protein complexes.

Hoopmann MR, Zelter A, Johnson RS, Riffle M, MacCoss MJ, Davis TN, Moritz RL.

J Proteome Res. 2015 May 1;14(5):2190-8. doi: 10.1021/pr501321h. Epub 2015 Apr 15.

PMID: 25812159

StPeter Label-free Quantitation

StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline.

Hoopmann MR, Winget JM, Mendoza L, Moritz RL.

J Proteome Res. 2018 Mar 2;17(3):1314-1320. doi: 10.1021/acs.jproteome.7b00786. Epub 2018 Feb 14.

PMID: 29400476

reSpect

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

Shteynberg D, Mendoza L, Hoopmann MR, Sun Z, Schmidt F, Deutsch EW, Moritz RL.

J Am Soc Mass Spectrom. 2015 Nov;26(11):1837-47. doi: 10.1007/s13361-015-1252-5. Epub 2015 Sep 29.

PMID: 26419769

THISP Human Sequence Databases

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL.

J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12.

PMID: 27577934

Proteomics Informatics Review

Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.

Deutsch EW, Lam H, Aebersold R.

Physiol Genomics. 2008 Mar 14;33(1):18-25. doi: 10.1152/physiolgenomics.00298.2007. Epub 2008 Jan 22. Review.

PMID: 18212004

SpectraST - Library Searching

Development and validation of a spectral library searching method for peptide identification from MS/MS.

Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R.

Proteomics. 2007 Mar;7(5):655-67.

PMID: 17295354

SpectraST - Library Building

Building consensus spectral libraries for peptide identification in proteomics.

Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R.

Nat Methods. 2008 Oct;5(10):873-5. doi: 10.1038/nmeth.1254. Epub 2008 Sep 21.

PMID: 18806791

SpectraST - Artificial Decoys

Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics.

Lam H, Deutsch EW, Aebersold R.

J Proteome Res. 2010 Jan;9(1):605-10. doi: 10.1021/pr900947u.

PMID: 19916561

Mass Spectrometry File Formats in General

File formats commonly used in mass spectrometry proteomics.

Deutsch EW.

Mol Cell Proteomics. 2012 Dec;11(12):1612-21. doi: 10.1074/mcp.R112.019695. Epub 2012 Sep 6.

PMID: 22956731

pepXML and protXML Initial Paper

A uniform proteomics MS/MS analysis platform utilizing open XML file formats.

Keller A, Eng J, Zhang N, Li XJ, Aebersold R.

Mol Syst Biol. 2005;1:2005.0017. Epub 2005 Aug 2.

PMID: 16729052

pepXML for Cross-linking Data

An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results.

Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL.

J Am Soc Mass Spectrom. 2016 Nov;27(11):1728-1734. Epub 2016 Jul 28.

PMID: 27469004

mzXML

A common open representation of mass spectrometry data and its application to proteomics research.

Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R.

Nat Biotechnol. 2004 Nov;22(11):1459-66.

PMID: 15529173

TPP on Amazon Web Services

Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline.

Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL.

Mol Cell Proteomics. 2015 Feb;14(2):399-404. doi: 10.1074/mcp.O114.043380. Epub 2014 Nov 23.

PMID: 25418363

Hydra

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.

Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J.

BMC Bioinformatics. 2012 Dec 5;13:324. doi: 10.1186/1471-2105-13-324.

PMID: 23216909

ETD analysis

Trans-Proteomic Pipeline supports and improves analysis of electron transfer dissociation data sets.

Deutsch EW, Shteynberg D, Lam H, Sun Z, Eng JK, Carapito C, von Haller PD, Tasman N, Mendoza L, Farrah T, Aebersold R.

Proteomics. 2010 Mar;10(6):1190-5. doi: 10.1002/pmic.200900567.

PMID: 20082347